First off: Andalites
How does their food (grass and stuff) get from the base of their four hooves/feet into their body? Does the "esophagus" in each leg somehow travel around the bone? Does it curl around the bone or just go straight up the side? Or does it go through the middle of the bone, in the center which is hollow? Do they have a four-chamberd stomach? One for each leg? Ruminant animals like cows and herbivores (look it up on Wikipedia:
http://en.wikipedia.org/wiki/Ruminant) have chambered stomachs like this, and Andalites are herbivores, right?
It's been stated that Andalites have two hearts. Obviously, one is in their upper torso, where a human's heart would be. The other heart, I think, is in their lower torso, like a horse's would be. They need two hearts for the extra energy that their large bodies require (running and quick-reflex tail fighting). Obviously, they have a trachea/windpipe running from their nose to their lungs (2), which are larger than a human's lungs. (I suspect that fantasy centaurs have larger lungs, too, but I'm not sure about how many hearts a centaur would have. Sorry, I'm digressing.)
As for their stalk eyes, I'm pretty sure that they have three layers. The very center of the stalk eye's stalk is optical nerve, which is directly referenced at the end of
The Andalite Chronicles, going directly to the brain, like any normal optic nerve should. The next layer going out is muscle, to move the eyes around. Last, of course, is the skin layer. But how do the eyeballs themselves actually attach to the stalks?
Last note on Andalites: Their upper torso contains two slightly-larger-than-human lungs, a heart, and maybe a pancreas and other respiratory/endocrine organs. Their lower body contains at least one stomach, possibly divided into four parts or four separate stomachs; one heart, a liver, two kidneys, other horse-like organs, and anything related to the digestive, endocrine, and reproductive systems.
Now, for the Hork-Bajir:
We already know they have two hearts. Since they have only one torso (that's human-shaped like a human's), both hearts must go here. I'm thinking they go behind the lungs, which are also larger than a human's. (They are bigger and taller - 7 to 9 feet, if I remember correctly.)
Of course, their stomachs are larger and designed to digest tree bark. (Are there any Earth animals that eat tree bark? Do beavers count?) Other than that, I can't speculate much. They have all the normal body systems you would expect: digestive, skeletal, muscular, circulatory, respiratory, endocrine, reproductive...
Lastly, Taxxons:
Not much to say here, other than that their skin is pretty thin, and their digestive system is probably primarily one long tube. Wait, what am I saying? Most vertebrate digestive systems are tubes. Taxxons' would have less curves. Do Taxxons have a skeletal system? Bones or a backbone? Are they really just big bags of guts?
Speaking of bones, I've always wanted someone to draw Andalite and Hork-Bajir skeletons. That would be so cool to see. I've seen centaur skeletons before (I think there's a deviantART group dedicated to that!), and everyone's seen human skeletons. The only thing that you'd need to really think about is what the Hork-Bajir skull looks like (where are the ear holes?), holes in the top of the Andalite skull (for you know what), possible bones in the Andalite tail?
(seriously, does the Andalite tail have bones, or is it just muscle? Remember - Samilin-Corrath-Gahar chopped off Harelin-Frodlin-Sirinial's tail, and Mertil-Iscar-Elmand's been missing his for a while now), and whether Hork-Bajir blades are made of sharp bone or if they're just really hard and sharp plastic-like flesh.
You know, after some quick research on Wikipedia, I'm pretty sure that Hork-Bajir blades are made of either
keratin or
chitin. Look 'em up! And welcome to Dogman15's alien biology discussion.
P.S. - This site's "spell check" thing needs a serious overhaul if it's saying words like "human's", "four-chambered", "Andalite" and "Hork-Bajir" are spelled incorectly/not even words.